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Question: How to convert from a .txt to a .maf file?
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gravatar for ksanchez1296
12 months ago by
ksanchez1296 • 0
ksanchez1296 • 0 wrote:

I have created a mutation annotation format (maf)-like text file and need to convert it into a .maf file for further analysis. Is there any way to do this conversion using a software or in R? There doesn't seem to be much information going from a .txt -> .maf. Any help would be greatly appreciated! I'm at a roadblock until I can figure this out.
bioinformatics txt tcga R maf • 891 views
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modified 12 months ago by Kevin Blighe ♦ 41k • written 12 months ago by ksanchez1296 • 0
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gravatar for Kevin Blighe
12 months ago by
Kevin Blighe ♦ 41k
Kevin Blighe ♦ 41k wrote:

Your TXT file may already fit the MAF format specification if you have the required columns. You have not indicated the columns that you already have, so, I (and no-one else) can say for definite. Keep in mind that MAF files are plain text, tab-delimited, and have specific column names. The TXT extension itself usually indicates that a file is plain text but says nothing about the structure / arrangement of the data inside.

You can check here whether or not your file is already in the MAF format (see Table 1): Mutation Annotation Format (MAF) Specification

On that same page, see the information under the heading 'MAF file checks'.

Keep further in mind that the MAF format was created as a result of the TCGA project, so, it is tailoured for cancer.

Kevin
ADD COMMENT • link written 12 months ago by Kevin Blighe ♦ 41k

There is also a different MAF format that predates MAF you are referring to.

ADD REPLY • link written 12 months ago by genomax ♦ 65k
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